Wheel bearing noise usually just escalates with speed. Normally a wheel bearing noise can be changed by cruising at a speed where it's quite loud, then swerving a bit side to side, this changes the load on each bearing and if the noise changes you can be more certain it's wheel bearing related. Most transfer cases do use a large chain, and yes they can get worn and start rubbing on the cases etc. Running the truck on a hoist using a stethoscope should locate the area of the noise pretty easily. The noise growing when accelerating is odd, the mechanic may be correct.
In reference to the transfer case, not many companies rebuild transfer cases? Remove and replace only?
It's a 99, there is no market for it. I believe we used to take them apart ourselves on some chevy's and just replace the chains. Not a huge deal really if everything else looked ok.